Multiple sequence alignment - TraesCS4A01G141700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G141700 chr4A 100.000 3650 0 0 1 3650 222560261 222556612 0.000000e+00 6741.0
1 TraesCS4A01G141700 chr4B 94.963 3236 103 18 448 3650 286072678 286075886 0.000000e+00 5018.0
2 TraesCS4A01G141700 chr4B 90.837 251 21 2 1 250 286072236 286072485 5.840000e-88 335.0
3 TraesCS4A01G141700 chr4B 95.506 89 4 0 1 89 482656345 482656433 3.800000e-30 143.0
4 TraesCS4A01G141700 chr4B 89.908 109 10 1 353 460 612274830 612274938 4.910000e-29 139.0
5 TraesCS4A01G141700 chr4B 93.258 89 6 0 1 89 384839230 384839142 8.220000e-27 132.0
6 TraesCS4A01G141700 chr4B 100.000 32 0 0 100 131 384839220 384839189 3.940000e-05 60.2
7 TraesCS4A01G141700 chr4D 96.942 2060 55 5 1293 3350 251525111 251523058 0.000000e+00 3448.0
8 TraesCS4A01G141700 chr4D 94.527 804 23 9 448 1239 251526167 251525373 0.000000e+00 1221.0
9 TraesCS4A01G141700 chr4D 96.732 306 7 1 3345 3650 251522967 251522665 1.170000e-139 507.0
10 TraesCS4A01G141700 chr4D 94.203 207 12 0 1 207 251526424 251526218 2.120000e-82 316.0
11 TraesCS4A01G141700 chr4D 95.238 105 5 0 206 310 490940140 490940036 2.250000e-37 167.0
12 TraesCS4A01G141700 chr4D 89.565 115 10 2 347 460 482704108 482704221 1.060000e-30 145.0
13 TraesCS4A01G141700 chr4D 90.090 111 10 1 342 451 301749635 301749745 3.800000e-30 143.0
14 TraesCS4A01G141700 chr4D 87.850 107 13 0 353 459 274741045 274740939 3.830000e-25 126.0
15 TraesCS4A01G141700 chr4D 98.305 59 1 0 299 357 251526221 251526163 1.790000e-18 104.0
16 TraesCS4A01G141700 chr7A 94.286 105 6 0 205 309 238526216 238526320 1.050000e-35 161.0
17 TraesCS4A01G141700 chr7A 91.743 109 8 1 205 312 73807270 73807162 2.270000e-32 150.0
18 TraesCS4A01G141700 chr7A 90.741 108 10 0 344 451 73807279 73807172 1.060000e-30 145.0
19 TraesCS4A01G141700 chr2B 95.876 97 4 0 206 302 63293187 63293091 1.360000e-34 158.0
20 TraesCS4A01G141700 chr2B 92.453 106 7 1 197 302 439316891 439316995 2.270000e-32 150.0
21 TraesCS4A01G141700 chr2B 87.069 116 12 2 354 469 719528564 719528676 1.060000e-25 128.0
22 TraesCS4A01G141700 chr1D 94.898 98 5 0 206 303 209519496 209519399 1.760000e-33 154.0
23 TraesCS4A01G141700 chr1D 86.614 127 13 4 178 302 37458203 37458327 1.770000e-28 137.0
24 TraesCS4A01G141700 chr7B 91.743 109 9 0 203 311 589348418 589348310 6.310000e-33 152.0
25 TraesCS4A01G141700 chr7B 92.784 97 7 0 354 450 194668092 194667996 1.370000e-29 141.0
26 TraesCS4A01G141700 chr7B 88.496 113 10 3 352 461 745161008 745161120 2.290000e-27 134.0
27 TraesCS4A01G141700 chr6D 91.429 105 9 0 346 450 355436596 355436700 1.060000e-30 145.0
28 TraesCS4A01G141700 chr6D 92.079 101 8 0 354 454 141924899 141924999 3.800000e-30 143.0
29 TraesCS4A01G141700 chr6B 95.506 89 4 0 1 89 563991321 563991233 3.800000e-30 143.0
30 TraesCS4A01G141700 chr6B 100.000 32 0 0 100 131 563991311 563991280 3.940000e-05 60.2
31 TraesCS4A01G141700 chr5B 93.617 94 6 0 1 94 93222601 93222508 1.370000e-29 141.0
32 TraesCS4A01G141700 chr5B 100.000 32 0 0 100 131 390869905 390869874 3.940000e-05 60.2
33 TraesCS4A01G141700 chr3B 90.000 110 8 3 352 461 487221374 487221480 4.910000e-29 139.0
34 TraesCS4A01G141700 chr3B 89.423 104 10 1 354 456 677753323 677753426 2.960000e-26 130.0
35 TraesCS4A01G141700 chrUn 85.507 138 12 7 197 334 50416673 50416544 1.770000e-28 137.0
36 TraesCS4A01G141700 chr3D 94.186 86 5 0 4 89 47653077 47652992 8.220000e-27 132.0
37 TraesCS4A01G141700 chr1B 93.258 89 6 0 1 89 576230310 576230398 8.220000e-27 132.0
38 TraesCS4A01G141700 chr1A 93.258 89 6 0 1 89 10077929 10077841 8.220000e-27 132.0
39 TraesCS4A01G141700 chr1A 97.059 34 1 0 98 131 283857355 283857388 1.420000e-04 58.4
40 TraesCS4A01G141700 chr3A 89.320 103 11 0 354 456 269394411 269394309 2.960000e-26 130.0
41 TraesCS4A01G141700 chr3A 87.736 106 12 1 354 458 12852620 12852515 4.950000e-24 122.0
42 TraesCS4A01G141700 chr3A 100.000 32 0 0 100 131 674276837 674276806 3.940000e-05 60.2
43 TraesCS4A01G141700 chr7D 97.059 34 1 0 98 131 262826035 262826068 1.420000e-04 58.4
44 TraesCS4A01G141700 chr2D 97.059 34 1 0 98 131 206697708 206697675 1.420000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G141700 chr4A 222556612 222560261 3649 True 6741.0 6741 100.0000 1 3650 1 chr4A.!!$R1 3649
1 TraesCS4A01G141700 chr4B 286072236 286075886 3650 False 2676.5 5018 92.9000 1 3650 2 chr4B.!!$F3 3649
2 TraesCS4A01G141700 chr4D 251522665 251526424 3759 True 1119.2 3448 96.1418 1 3650 5 chr4D.!!$R3 3649

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
966 1086 0.323087 TCACATTCTCCTCCCGTCGA 60.323 55.0 0.0 0.0 0.0 4.20 F
1263 1383 0.684805 TTCTCCTCTTCCTCGCCTCC 60.685 60.0 0.0 0.0 0.0 4.30 F
2106 2434 0.395173 ACGAAGCAGTTGGGGTGTTT 60.395 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 2122 0.035317 AACCACGCAGCTTGATCTCA 59.965 50.000 0.00 0.00 0.00 3.27 R
2484 2812 0.246360 TTCGCTCGGATTTGCTCAGA 59.754 50.000 0.00 0.00 0.00 3.27 R
3038 3367 1.275856 CAGAGAGCTCTATGGCCATCC 59.724 57.143 27.23 9.47 37.98 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 8.318412 TCAAGGACATGTACTATAATGTTGTGT 58.682 33.333 12.04 0.00 37.15 3.72
89 90 2.768253 TGGCGACATTGATGACTTCT 57.232 45.000 0.00 0.00 33.40 2.85
151 152 9.189156 ACTATATAAACCAAGCAACACATCATT 57.811 29.630 0.00 0.00 0.00 2.57
166 167 6.422333 ACACATCATTCCATATGTACCACAA 58.578 36.000 1.24 0.00 34.61 3.33
207 208 9.390795 CAAGCATGCATAGAATTAATCAAGTAC 57.609 33.333 21.98 0.00 0.00 2.73
215 216 6.163135 AGAATTAATCAAGTACTCCCTCCG 57.837 41.667 0.00 0.00 0.00 4.63
217 218 4.996788 TTAATCAAGTACTCCCTCCGTC 57.003 45.455 0.00 0.00 0.00 4.79
218 219 1.777941 ATCAAGTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
226 227 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
227 228 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
230 231 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
237 238 4.083484 CGTCCCAAAATAAGTGTCTCAACC 60.083 45.833 0.00 0.00 0.00 3.77
240 241 6.713450 GTCCCAAAATAAGTGTCTCAACCTTA 59.287 38.462 0.00 0.00 0.00 2.69
241 242 6.940298 TCCCAAAATAAGTGTCTCAACCTTAG 59.060 38.462 0.00 0.00 0.00 2.18
242 243 6.715264 CCCAAAATAAGTGTCTCAACCTTAGT 59.285 38.462 0.00 0.00 0.00 2.24
243 244 7.881232 CCCAAAATAAGTGTCTCAACCTTAGTA 59.119 37.037 0.00 0.00 0.00 1.82
250 297 6.514063 AGTGTCTCAACCTTAGTACAACTTC 58.486 40.000 0.00 0.00 0.00 3.01
251 298 5.695363 GTGTCTCAACCTTAGTACAACTTCC 59.305 44.000 0.00 0.00 0.00 3.46
257 304 8.345724 TCAACCTTAGTACAACTTCCTACTAG 57.654 38.462 0.00 0.00 29.27 2.57
258 305 8.166061 TCAACCTTAGTACAACTTCCTACTAGA 58.834 37.037 0.00 0.00 29.27 2.43
259 306 8.460428 CAACCTTAGTACAACTTCCTACTAGAG 58.540 40.741 0.00 0.00 29.27 2.43
272 319 9.230122 ACTTCCTACTAGAGTTAGTACAAAGTC 57.770 37.037 0.00 0.00 37.40 3.01
273 320 9.228949 CTTCCTACTAGAGTTAGTACAAAGTCA 57.771 37.037 0.00 0.00 40.55 3.41
274 321 9.578576 TTCCTACTAGAGTTAGTACAAAGTCAA 57.421 33.333 0.00 0.00 40.55 3.18
275 322 9.228949 TCCTACTAGAGTTAGTACAAAGTCAAG 57.771 37.037 0.00 0.00 40.55 3.02
276 323 9.228949 CCTACTAGAGTTAGTACAAAGTCAAGA 57.771 37.037 0.00 0.00 40.55 3.02
279 326 8.351461 ACTAGAGTTAGTACAAAGTCAAGACAC 58.649 37.037 0.00 0.00 38.35 3.67
280 327 7.349412 AGAGTTAGTACAAAGTCAAGACACT 57.651 36.000 2.72 0.00 32.24 3.55
289 380 6.805713 ACAAAGTCAAGACACTTATTTTGGG 58.194 36.000 2.72 0.00 35.45 4.12
296 387 3.581332 AGACACTTATTTTGGGACGGAGA 59.419 43.478 0.00 0.00 0.00 3.71
336 427 6.015434 ACTGAATAGAATCAACAACCAAACCC 60.015 38.462 0.00 0.00 0.00 4.11
364 455 4.986783 TCGATATGATGTACTCCCTCTGT 58.013 43.478 0.00 0.00 0.00 3.41
365 456 5.004448 TCGATATGATGTACTCCCTCTGTC 58.996 45.833 0.00 0.00 0.00 3.51
366 457 4.156922 CGATATGATGTACTCCCTCTGTCC 59.843 50.000 0.00 0.00 0.00 4.02
367 458 2.160721 TGATGTACTCCCTCTGTCCC 57.839 55.000 0.00 0.00 0.00 4.46
368 459 1.361197 TGATGTACTCCCTCTGTCCCA 59.639 52.381 0.00 0.00 0.00 4.37
369 460 2.225522 TGATGTACTCCCTCTGTCCCAA 60.226 50.000 0.00 0.00 0.00 4.12
370 461 2.409064 TGTACTCCCTCTGTCCCAAA 57.591 50.000 0.00 0.00 0.00 3.28
371 462 2.696775 TGTACTCCCTCTGTCCCAAAA 58.303 47.619 0.00 0.00 0.00 2.44
372 463 3.256704 TGTACTCCCTCTGTCCCAAAAT 58.743 45.455 0.00 0.00 0.00 1.82
373 464 4.431378 TGTACTCCCTCTGTCCCAAAATA 58.569 43.478 0.00 0.00 0.00 1.40
374 465 4.847512 TGTACTCCCTCTGTCCCAAAATAA 59.152 41.667 0.00 0.00 0.00 1.40
375 466 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
376 467 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
377 468 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
378 469 3.655777 TCCCTCTGTCCCAAAATAAGTGT 59.344 43.478 0.00 0.00 0.00 3.55
379 470 4.010349 CCCTCTGTCCCAAAATAAGTGTC 58.990 47.826 0.00 0.00 0.00 3.67
380 471 4.263506 CCCTCTGTCCCAAAATAAGTGTCT 60.264 45.833 0.00 0.00 0.00 3.41
381 472 4.938226 CCTCTGTCCCAAAATAAGTGTCTC 59.062 45.833 0.00 0.00 0.00 3.36
382 473 5.513094 CCTCTGTCCCAAAATAAGTGTCTCA 60.513 44.000 0.00 0.00 0.00 3.27
383 474 5.935945 TCTGTCCCAAAATAAGTGTCTCAA 58.064 37.500 0.00 0.00 0.00 3.02
384 475 5.763204 TCTGTCCCAAAATAAGTGTCTCAAC 59.237 40.000 0.00 0.00 0.00 3.18
385 476 4.825085 TGTCCCAAAATAAGTGTCTCAACC 59.175 41.667 0.00 0.00 0.00 3.77
386 477 5.070685 GTCCCAAAATAAGTGTCTCAACCT 58.929 41.667 0.00 0.00 0.00 3.50
387 478 5.535030 GTCCCAAAATAAGTGTCTCAACCTT 59.465 40.000 0.00 0.00 0.00 3.50
388 479 6.713450 GTCCCAAAATAAGTGTCTCAACCTTA 59.287 38.462 0.00 0.00 0.00 2.69
389 480 6.940298 TCCCAAAATAAGTGTCTCAACCTTAG 59.060 38.462 0.00 0.00 0.00 2.18
390 481 6.715264 CCCAAAATAAGTGTCTCAACCTTAGT 59.285 38.462 0.00 0.00 0.00 2.24
391 482 7.881232 CCCAAAATAAGTGTCTCAACCTTAGTA 59.119 37.037 0.00 0.00 0.00 1.82
392 483 8.718734 CCAAAATAAGTGTCTCAACCTTAGTAC 58.281 37.037 0.00 0.00 0.00 2.73
393 484 9.268268 CAAAATAAGTGTCTCAACCTTAGTACA 57.732 33.333 0.00 0.00 0.00 2.90
394 485 9.841295 AAAATAAGTGTCTCAACCTTAGTACAA 57.159 29.630 0.00 0.00 0.00 2.41
395 486 9.490379 AAATAAGTGTCTCAACCTTAGTACAAG 57.510 33.333 0.00 0.00 0.00 3.16
396 487 6.481434 AAGTGTCTCAACCTTAGTACAAGT 57.519 37.500 0.00 0.00 0.00 3.16
397 488 6.481434 AGTGTCTCAACCTTAGTACAAGTT 57.519 37.500 0.00 0.00 0.00 2.66
398 489 6.885922 AGTGTCTCAACCTTAGTACAAGTTT 58.114 36.000 0.00 0.00 0.00 2.66
399 490 6.761714 AGTGTCTCAACCTTAGTACAAGTTTG 59.238 38.462 0.00 2.73 0.00 2.93
400 491 6.537660 GTGTCTCAACCTTAGTACAAGTTTGT 59.462 38.462 11.88 2.75 44.86 2.83
401 492 7.707893 GTGTCTCAACCTTAGTACAAGTTTGTA 59.292 37.037 11.88 0.73 42.35 2.41
426 517 8.461249 ACTAGAGTTAGTACAAACTTGAGACA 57.539 34.615 0.00 0.00 39.78 3.41
427 518 8.351461 ACTAGAGTTAGTACAAACTTGAGACAC 58.649 37.037 0.00 0.00 39.78 3.67
428 519 7.349412 AGAGTTAGTACAAACTTGAGACACT 57.651 36.000 0.00 0.00 39.78 3.55
429 520 7.783042 AGAGTTAGTACAAACTTGAGACACTT 58.217 34.615 0.00 0.00 39.78 3.16
430 521 8.910944 AGAGTTAGTACAAACTTGAGACACTTA 58.089 33.333 0.00 0.00 39.78 2.24
431 522 9.694137 GAGTTAGTACAAACTTGAGACACTTAT 57.306 33.333 0.00 0.00 39.78 1.73
441 532 9.511144 AAACTTGAGACACTTATTTTAAAACCG 57.489 29.630 1.97 0.00 0.00 4.44
442 533 8.441312 ACTTGAGACACTTATTTTAAAACCGA 57.559 30.769 1.97 0.00 0.00 4.69
443 534 8.557029 ACTTGAGACACTTATTTTAAAACCGAG 58.443 33.333 1.97 4.41 0.00 4.63
444 535 7.429636 TGAGACACTTATTTTAAAACCGAGG 57.570 36.000 1.97 0.00 0.00 4.63
445 536 6.428771 TGAGACACTTATTTTAAAACCGAGGG 59.571 38.462 1.97 5.41 0.00 4.30
446 537 6.536447 AGACACTTATTTTAAAACCGAGGGA 58.464 36.000 1.97 0.00 0.00 4.20
447 538 6.653740 AGACACTTATTTTAAAACCGAGGGAG 59.346 38.462 1.97 0.00 0.00 4.30
448 539 6.301486 ACACTTATTTTAAAACCGAGGGAGT 58.699 36.000 1.97 0.00 0.00 3.85
449 540 7.452562 ACACTTATTTTAAAACCGAGGGAGTA 58.547 34.615 1.97 0.00 0.00 2.59
450 541 7.938490 ACACTTATTTTAAAACCGAGGGAGTAA 59.062 33.333 1.97 0.00 0.00 2.24
451 542 8.953313 CACTTATTTTAAAACCGAGGGAGTAAT 58.047 33.333 1.97 0.00 0.00 1.89
456 547 3.366052 AAACCGAGGGAGTAATTGCAT 57.634 42.857 0.00 0.00 0.00 3.96
770 885 5.618236 GTTTAGTTAGGGTTTCTGTGAGGT 58.382 41.667 0.00 0.00 0.00 3.85
787 902 9.444600 TCTGTGAGGTTTGGATAATAACTTTAC 57.555 33.333 0.00 0.00 0.00 2.01
788 903 8.259049 TGTGAGGTTTGGATAATAACTTTACG 57.741 34.615 0.00 0.00 0.00 3.18
797 916 8.428186 TGGATAATAACTTTACGAAAAGCGAT 57.572 30.769 0.00 0.00 45.06 4.58
810 929 4.509970 CGAAAAGCGATAGAGAGAGAGAGA 59.490 45.833 0.00 0.00 44.57 3.10
830 949 8.543774 AGAGAGAAGATCATGGCTTTTAACTTA 58.456 33.333 0.00 0.00 0.00 2.24
966 1086 0.323087 TCACATTCTCCTCCCGTCGA 60.323 55.000 0.00 0.00 0.00 4.20
1003 1123 1.299648 CCACGGATCACCACCATGT 59.700 57.895 0.00 0.00 35.59 3.21
1165 1285 2.362503 TCCTGTCGCTCGTCCCAT 60.363 61.111 0.00 0.00 0.00 4.00
1263 1383 0.684805 TTCTCCTCTTCCTCGCCTCC 60.685 60.000 0.00 0.00 0.00 4.30
1267 1387 2.683933 TCTTCCTCGCCTCCCACC 60.684 66.667 0.00 0.00 0.00 4.61
1269 1389 2.203938 TTCCTCGCCTCCCACCTT 60.204 61.111 0.00 0.00 0.00 3.50
1353 1681 2.580815 CTCCAGCCACATCTCGCA 59.419 61.111 0.00 0.00 0.00 5.10
1770 2098 2.037049 TTTGCGCATGGGATGGGT 59.963 55.556 12.75 0.00 44.22 4.51
1794 2122 1.122019 AGGCCCTTCGTGTCTTCAGT 61.122 55.000 0.00 0.00 0.00 3.41
1845 2173 4.394439 TGTAGTCACTTACAACACAGCA 57.606 40.909 0.00 0.00 30.94 4.41
1851 2179 3.118775 TCACTTACAACACAGCACTCACT 60.119 43.478 0.00 0.00 0.00 3.41
1872 2200 4.221924 ACTGGTTTATGTAAAATGGGCCAC 59.778 41.667 9.28 0.00 0.00 5.01
1886 2214 4.892379 CCACATTGCCGATGCGCG 62.892 66.667 0.00 0.00 41.78 6.86
2106 2434 0.395173 ACGAAGCAGTTGGGGTGTTT 60.395 50.000 0.00 0.00 0.00 2.83
2121 2449 3.492337 GGTGTTTGAGGGAATGGTTACA 58.508 45.455 0.00 0.00 0.00 2.41
2281 2609 1.948834 CACTCATTGACACCTTGTGCA 59.051 47.619 0.00 0.00 36.98 4.57
2295 2623 1.973812 GTGCAAGGAAGGGCAGGTC 60.974 63.158 0.00 0.00 41.35 3.85
2453 2781 5.007626 TGTTGAAGAACAATCTGAAACCTCG 59.992 40.000 0.00 0.00 39.20 4.63
2484 2812 3.499918 CGTTCAATTCTTTGCTGGAGTCT 59.500 43.478 0.00 0.00 32.61 3.24
2490 2818 1.274728 TCTTTGCTGGAGTCTCTGAGC 59.725 52.381 14.23 14.23 0.00 4.26
2603 2931 8.713206 ACTTGTTGATAAGTTATGCACAGGCAT 61.713 37.037 7.39 7.39 45.41 4.40
2738 3066 9.442047 TTGAGAAATGTTTTTATTGGTGTTGTT 57.558 25.926 0.00 0.00 0.00 2.83
2861 3190 5.819901 CCATTCCAGTAAATCTTGGAGAGAC 59.180 44.000 0.00 0.00 37.17 3.36
2864 3193 5.333581 TCCAGTAAATCTTGGAGAGACAGA 58.666 41.667 0.00 0.00 37.17 3.41
2913 3242 1.617850 CAGCTCTGAGAGGTTGTGACT 59.382 52.381 12.08 0.00 38.40 3.41
2921 3250 1.069823 AGAGGTTGTGACTGCAGTGAG 59.930 52.381 27.27 0.00 0.00 3.51
2938 3267 1.303309 GAGCAGCGTTGATGGCTAAT 58.697 50.000 2.38 0.00 39.08 1.73
2939 3268 2.158971 TGAGCAGCGTTGATGGCTAATA 60.159 45.455 2.38 0.00 39.08 0.98
2983 3312 0.452987 CAAATGCCTGTGATCGTGGG 59.547 55.000 0.00 0.00 0.00 4.61
3001 3330 2.846206 TGGGGATCTATTGAACAGCACT 59.154 45.455 0.00 0.00 0.00 4.40
3115 3444 1.490490 GCATCTCCATTCCCAGGTGTA 59.510 52.381 0.00 0.00 0.00 2.90
3120 3449 3.054434 TCTCCATTCCCAGGTGTACATTG 60.054 47.826 0.00 0.83 0.00 2.82
3439 3864 9.857656 AGATCATATGTGTCCAATTGTCTTAAT 57.142 29.630 4.43 0.00 0.00 1.40
3480 3905 6.718294 ACCGTCCTAATTTAAAGGATCAACT 58.282 36.000 0.00 0.00 44.79 3.16
3491 3916 7.801893 TTAAAGGATCAACTACCTAACTGGA 57.198 36.000 0.00 0.00 39.71 3.86
3537 3962 0.833287 CACCCATAGGTCCAGTCCAG 59.167 60.000 0.00 0.00 46.45 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 4.442706 ACATGTCCTTGATGACGGTAATC 58.557 43.478 0.00 0.00 38.11 1.75
50 51 3.559655 CCATCACTTGTTCGAACACTTGA 59.440 43.478 29.56 29.56 38.92 3.02
89 90 8.879227 TGATGAGGGTAATGTACATCATATCAA 58.121 33.333 9.23 0.00 41.12 2.57
151 152 5.284861 AGCGTAATTGTGGTACATATGGA 57.715 39.130 7.80 0.00 44.52 3.41
166 167 4.150451 GCATGCTTGTTTTCAAAGCGTAAT 59.850 37.500 11.37 0.00 39.47 1.89
207 208 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
215 216 5.070685 AGGTTGAGACACTTATTTTGGGAC 58.929 41.667 0.00 0.00 0.00 4.46
217 218 6.715264 ACTAAGGTTGAGACACTTATTTTGGG 59.285 38.462 0.00 0.00 0.00 4.12
218 219 7.745620 ACTAAGGTTGAGACACTTATTTTGG 57.254 36.000 0.00 0.00 0.00 3.28
226 227 6.462628 GGAAGTTGTACTAAGGTTGAGACACT 60.463 42.308 0.00 0.00 0.00 3.55
227 228 5.695363 GGAAGTTGTACTAAGGTTGAGACAC 59.305 44.000 0.00 0.00 0.00 3.67
230 231 7.008941 AGTAGGAAGTTGTACTAAGGTTGAGA 58.991 38.462 0.00 0.00 0.00 3.27
240 241 9.665719 GTACTAACTCTAGTAGGAAGTTGTACT 57.334 37.037 20.28 1.21 40.54 2.73
241 242 9.442047 TGTACTAACTCTAGTAGGAAGTTGTAC 57.558 37.037 20.48 20.48 40.54 2.90
243 244 8.930846 TTGTACTAACTCTAGTAGGAAGTTGT 57.069 34.615 12.37 10.77 40.54 3.32
250 297 9.228949 TCTTGACTTTGTACTAACTCTAGTAGG 57.771 37.037 0.00 0.00 40.54 3.18
257 304 9.694137 ATAAGTGTCTTGACTTTGTACTAACTC 57.306 33.333 2.35 0.00 37.38 3.01
272 319 4.069304 TCCGTCCCAAAATAAGTGTCTTG 58.931 43.478 0.00 0.00 0.00 3.02
273 320 4.041198 TCTCCGTCCCAAAATAAGTGTCTT 59.959 41.667 0.00 0.00 0.00 3.01
274 321 3.581332 TCTCCGTCCCAAAATAAGTGTCT 59.419 43.478 0.00 0.00 0.00 3.41
275 322 3.933332 CTCTCCGTCCCAAAATAAGTGTC 59.067 47.826 0.00 0.00 0.00 3.67
276 323 3.581332 TCTCTCCGTCCCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
279 326 4.473477 ACTCTCTCCGTCCCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
280 327 6.555463 ATTACTCTCTCCGTCCCAAAATAA 57.445 37.500 0.00 0.00 0.00 1.40
289 380 7.441760 TCAGTCTTATGTATTACTCTCTCCGTC 59.558 40.741 0.00 0.00 0.00 4.79
357 448 4.010349 GACACTTATTTTGGGACAGAGGG 58.990 47.826 0.00 0.00 42.39 4.30
358 449 4.911390 AGACACTTATTTTGGGACAGAGG 58.089 43.478 0.00 0.00 42.39 3.69
359 450 5.551233 TGAGACACTTATTTTGGGACAGAG 58.449 41.667 0.00 0.00 42.39 3.35
360 451 5.560722 TGAGACACTTATTTTGGGACAGA 57.439 39.130 0.00 0.00 42.39 3.41
361 452 5.048713 GGTTGAGACACTTATTTTGGGACAG 60.049 44.000 0.00 0.00 42.39 3.51
362 453 4.825085 GGTTGAGACACTTATTTTGGGACA 59.175 41.667 0.00 0.00 0.00 4.02
363 454 5.070685 AGGTTGAGACACTTATTTTGGGAC 58.929 41.667 0.00 0.00 0.00 4.46
364 455 5.319043 AGGTTGAGACACTTATTTTGGGA 57.681 39.130 0.00 0.00 0.00 4.37
365 456 6.715264 ACTAAGGTTGAGACACTTATTTTGGG 59.285 38.462 0.00 0.00 0.00 4.12
366 457 7.745620 ACTAAGGTTGAGACACTTATTTTGG 57.254 36.000 0.00 0.00 0.00 3.28
367 458 9.268268 TGTACTAAGGTTGAGACACTTATTTTG 57.732 33.333 0.00 0.00 0.00 2.44
368 459 9.841295 TTGTACTAAGGTTGAGACACTTATTTT 57.159 29.630 0.00 0.00 0.00 1.82
369 460 9.490379 CTTGTACTAAGGTTGAGACACTTATTT 57.510 33.333 0.00 0.00 0.00 1.40
370 461 8.648693 ACTTGTACTAAGGTTGAGACACTTATT 58.351 33.333 9.05 0.00 0.00 1.40
371 462 8.191534 ACTTGTACTAAGGTTGAGACACTTAT 57.808 34.615 9.05 0.00 0.00 1.73
372 463 7.592885 ACTTGTACTAAGGTTGAGACACTTA 57.407 36.000 9.05 0.00 0.00 2.24
373 464 6.481434 ACTTGTACTAAGGTTGAGACACTT 57.519 37.500 9.05 0.00 0.00 3.16
374 465 6.481434 AACTTGTACTAAGGTTGAGACACT 57.519 37.500 9.05 0.00 0.00 3.55
375 466 6.537660 ACAAACTTGTACTAAGGTTGAGACAC 59.462 38.462 27.69 0.00 45.30 3.67
376 467 6.646267 ACAAACTTGTACTAAGGTTGAGACA 58.354 36.000 27.69 0.00 45.30 3.41
400 491 9.565090 TGTCTCAAGTTTGTACTAACTCTAGTA 57.435 33.333 20.50 12.21 39.23 1.82
401 492 8.351461 GTGTCTCAAGTTTGTACTAACTCTAGT 58.649 37.037 20.50 4.98 41.43 2.57
402 493 8.569641 AGTGTCTCAAGTTTGTACTAACTCTAG 58.430 37.037 20.50 18.91 37.37 2.43
403 494 8.461249 AGTGTCTCAAGTTTGTACTAACTCTA 57.539 34.615 20.50 11.97 37.37 2.43
404 495 7.349412 AGTGTCTCAAGTTTGTACTAACTCT 57.651 36.000 20.50 10.30 37.37 3.24
405 496 9.694137 ATAAGTGTCTCAAGTTTGTACTAACTC 57.306 33.333 20.50 10.09 37.37 3.01
415 506 9.511144 CGGTTTTAAAATAAGTGTCTCAAGTTT 57.489 29.630 3.52 0.00 0.00 2.66
416 507 8.895737 TCGGTTTTAAAATAAGTGTCTCAAGTT 58.104 29.630 3.52 0.00 0.00 2.66
417 508 8.441312 TCGGTTTTAAAATAAGTGTCTCAAGT 57.559 30.769 3.52 0.00 0.00 3.16
418 509 8.015658 CCTCGGTTTTAAAATAAGTGTCTCAAG 58.984 37.037 3.52 0.00 0.00 3.02
419 510 7.040961 CCCTCGGTTTTAAAATAAGTGTCTCAA 60.041 37.037 3.52 0.00 0.00 3.02
420 511 6.428771 CCCTCGGTTTTAAAATAAGTGTCTCA 59.571 38.462 3.52 0.00 0.00 3.27
421 512 6.652062 TCCCTCGGTTTTAAAATAAGTGTCTC 59.348 38.462 3.52 0.00 0.00 3.36
422 513 6.536447 TCCCTCGGTTTTAAAATAAGTGTCT 58.464 36.000 3.52 0.00 0.00 3.41
423 514 6.429078 ACTCCCTCGGTTTTAAAATAAGTGTC 59.571 38.462 3.52 0.00 0.00 3.67
424 515 6.301486 ACTCCCTCGGTTTTAAAATAAGTGT 58.699 36.000 3.52 0.01 0.00 3.55
425 516 6.812879 ACTCCCTCGGTTTTAAAATAAGTG 57.187 37.500 3.52 0.73 0.00 3.16
426 517 9.524496 AATTACTCCCTCGGTTTTAAAATAAGT 57.476 29.630 3.52 3.73 0.00 2.24
427 518 9.783256 CAATTACTCCCTCGGTTTTAAAATAAG 57.217 33.333 3.52 2.61 0.00 1.73
428 519 8.245491 GCAATTACTCCCTCGGTTTTAAAATAA 58.755 33.333 3.52 0.00 0.00 1.40
429 520 7.393796 TGCAATTACTCCCTCGGTTTTAAAATA 59.606 33.333 3.52 0.00 0.00 1.40
430 521 6.209788 TGCAATTACTCCCTCGGTTTTAAAAT 59.790 34.615 3.52 0.00 0.00 1.82
431 522 5.535406 TGCAATTACTCCCTCGGTTTTAAAA 59.465 36.000 0.00 0.00 0.00 1.52
432 523 5.071370 TGCAATTACTCCCTCGGTTTTAAA 58.929 37.500 0.00 0.00 0.00 1.52
433 524 4.653868 TGCAATTACTCCCTCGGTTTTAA 58.346 39.130 0.00 0.00 0.00 1.52
434 525 4.289238 TGCAATTACTCCCTCGGTTTTA 57.711 40.909 0.00 0.00 0.00 1.52
435 526 3.149005 TGCAATTACTCCCTCGGTTTT 57.851 42.857 0.00 0.00 0.00 2.43
436 527 2.871096 TGCAATTACTCCCTCGGTTT 57.129 45.000 0.00 0.00 0.00 3.27
437 528 2.643551 CATGCAATTACTCCCTCGGTT 58.356 47.619 0.00 0.00 0.00 4.44
438 529 1.747206 GCATGCAATTACTCCCTCGGT 60.747 52.381 14.21 0.00 0.00 4.69
439 530 0.947244 GCATGCAATTACTCCCTCGG 59.053 55.000 14.21 0.00 0.00 4.63
440 531 1.600957 CTGCATGCAATTACTCCCTCG 59.399 52.381 22.88 0.96 0.00 4.63
441 532 2.648059 ACTGCATGCAATTACTCCCTC 58.352 47.619 22.88 0.00 0.00 4.30
442 533 2.814805 ACTGCATGCAATTACTCCCT 57.185 45.000 22.88 0.00 0.00 4.20
443 534 3.947834 AGTTACTGCATGCAATTACTCCC 59.052 43.478 22.88 4.48 0.00 4.30
444 535 6.260936 ACATAGTTACTGCATGCAATTACTCC 59.739 38.462 22.30 7.07 0.00 3.85
445 536 7.251704 ACATAGTTACTGCATGCAATTACTC 57.748 36.000 22.30 10.71 0.00 2.59
446 537 8.731275 TTACATAGTTACTGCATGCAATTACT 57.269 30.769 22.29 22.29 0.00 2.24
447 538 9.385902 CATTACATAGTTACTGCATGCAATTAC 57.614 33.333 22.88 16.18 0.00 1.89
448 539 9.336171 TCATTACATAGTTACTGCATGCAATTA 57.664 29.630 22.88 12.93 0.00 1.40
449 540 8.224389 TCATTACATAGTTACTGCATGCAATT 57.776 30.769 22.88 14.01 0.00 2.32
450 541 7.806409 TCATTACATAGTTACTGCATGCAAT 57.194 32.000 22.88 15.39 0.00 3.56
451 542 7.806409 ATCATTACATAGTTACTGCATGCAA 57.194 32.000 22.88 4.63 0.00 4.08
494 585 2.417515 CGTAACTCTGGGGAGAAGAAGC 60.418 54.545 0.00 0.00 41.86 3.86
770 885 8.719648 TCGCTTTTCGTAAAGTTATTATCCAAA 58.280 29.630 14.86 0.00 42.25 3.28
787 902 4.509970 TCTCTCTCTCTCTATCGCTTTTCG 59.490 45.833 0.00 0.00 40.15 3.46
788 903 6.260050 TCTTCTCTCTCTCTCTATCGCTTTTC 59.740 42.308 0.00 0.00 0.00 2.29
792 911 4.955811 TCTTCTCTCTCTCTCTATCGCT 57.044 45.455 0.00 0.00 0.00 4.93
797 916 5.073554 AGCCATGATCTTCTCTCTCTCTCTA 59.926 44.000 0.00 0.00 0.00 2.43
830 949 2.594592 GAGGCCCACGTGTGCTTT 60.595 61.111 22.19 11.23 0.00 3.51
869 988 2.031157 CGCGAGGTTTTGACTTGGATTT 60.031 45.455 0.00 0.00 0.00 2.17
987 1107 1.602237 GGACATGGTGGTGATCCGT 59.398 57.895 0.00 0.00 36.30 4.69
1212 1332 2.960879 TTCAGGGGAGGGGAGGAGG 61.961 68.421 0.00 0.00 0.00 4.30
1398 1726 3.565214 TTGAGTGCGGGCAGGGAA 61.565 61.111 0.00 0.00 0.00 3.97
1584 1912 2.433145 CCACGTCGTGCAGCATCT 60.433 61.111 20.01 0.00 31.34 2.90
1794 2122 0.035317 AACCACGCAGCTTGATCTCA 59.965 50.000 0.00 0.00 0.00 3.27
1845 2173 5.185056 GCCCATTTTACATAAACCAGTGAGT 59.815 40.000 0.00 0.00 0.00 3.41
1851 2179 4.160329 TGTGGCCCATTTTACATAAACCA 58.840 39.130 0.00 0.00 0.00 3.67
1886 2214 1.544982 CCATCTCATCCCACATCTGCC 60.545 57.143 0.00 0.00 0.00 4.85
2106 2434 3.399644 TCCCTTTTGTAACCATTCCCTCA 59.600 43.478 0.00 0.00 0.00 3.86
2121 2449 6.438108 TGATCACATCATGTTCAATCCCTTTT 59.562 34.615 0.00 0.00 34.69 2.27
2281 2609 0.909610 TGATCGACCTGCCCTTCCTT 60.910 55.000 0.00 0.00 0.00 3.36
2289 2617 0.376152 CAACAGCATGATCGACCTGC 59.624 55.000 0.00 7.42 39.69 4.85
2295 2623 6.258727 AGGTAAGTAATTCAACAGCATGATCG 59.741 38.462 0.00 0.00 39.69 3.69
2484 2812 0.246360 TTCGCTCGGATTTGCTCAGA 59.754 50.000 0.00 0.00 0.00 3.27
2490 2818 2.032549 GTCATCCATTCGCTCGGATTTG 60.033 50.000 0.00 0.00 40.12 2.32
2603 2931 7.829211 CCTCCAACTTTTGAGGATAAGATACAA 59.171 37.037 3.45 0.00 36.99 2.41
2700 3028 9.820725 AAAAACATTTCTCAAAGACATCAATCA 57.179 25.926 0.00 0.00 0.00 2.57
2738 3066 7.230510 ACATAAGTCATTTGTGTAGCCTTTTGA 59.769 33.333 0.00 0.00 39.07 2.69
2777 3105 3.077359 GTCAAGTTCTTGGTCATCAGGG 58.923 50.000 11.82 0.00 0.00 4.45
2921 3250 3.499918 AGAATATTAGCCATCAACGCTGC 59.500 43.478 0.00 0.00 37.12 5.25
2938 3267 7.724061 GGATTATTACAGGGCCAAAGAAGAATA 59.276 37.037 6.18 0.00 0.00 1.75
2939 3268 6.551227 GGATTATTACAGGGCCAAAGAAGAAT 59.449 38.462 6.18 3.19 0.00 2.40
2983 3312 5.665459 ACTACAGTGCTGTTCAATAGATCC 58.335 41.667 10.28 0.00 41.83 3.36
2991 3320 3.895656 AGAAGGTACTACAGTGCTGTTCA 59.104 43.478 10.28 0.00 44.42 3.18
3038 3367 1.275856 CAGAGAGCTCTATGGCCATCC 59.724 57.143 27.23 9.47 37.98 3.51
3120 3449 2.165641 GGTTATTACAGGGCCAAAGCAC 59.834 50.000 6.18 0.00 45.63 4.40
3201 3530 3.119602 CGAAATACAGGAAGGACGAGACA 60.120 47.826 0.00 0.00 0.00 3.41
3254 3583 3.664486 CGTCGTAGTTCTCTTGACAACAG 59.336 47.826 0.00 0.00 32.14 3.16
3427 3852 8.253113 ACATTAGCTTGGGAATTAAGACAATTG 58.747 33.333 3.24 3.24 0.00 2.32
3439 3864 2.303600 ACGGTACACATTAGCTTGGGAA 59.696 45.455 0.00 0.00 0.00 3.97
3440 3865 1.903860 ACGGTACACATTAGCTTGGGA 59.096 47.619 0.00 0.00 0.00 4.37
3480 3905 7.458806 ACCATACCTTAAGTTTCCAGTTAGGTA 59.541 37.037 0.97 0.00 39.02 3.08
3491 3916 9.043548 AGTACACAGATACCATACCTTAAGTTT 57.956 33.333 0.97 0.00 0.00 2.66
3537 3962 5.067674 TGAATTTGCTATGCATGGAAGTACC 59.932 40.000 15.09 0.00 38.76 3.34


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.